He told the court he found "numerous occurrences'' of footwear impressions with a wavy pattern close to Mr Guy's body and his ute.
Blood was still flowing into one impression near Mr Guy's head while Mr Neale was at the scene.
"The impression was there before the blood flowed into it,'' he said.
Wavy prints were also found on the grass verge near Mr Guy's driveway and in a trail through a paddock that led to an old cow shed - from where Macdonald allegedly stole and killed three chocolate labrador puppies to throw investigators off the trail.
Mr Neale said casts were made of the footwear impressions and carefully removed and cleaned.
He did not have an item of footwear to compare the impressions with, so he studied the size and pattern of the impressions to determine the characteristics of the killer's shoes.
Impressions from Mr Guy's gumboots were examined to eliminate them from the inquiry.
The court also heard of the extensive search to determine the type of footwear that matched the impressions.
Detective Laurie Howell said officers visited dozens of sports, footwear and dive shops from Hawkes Bay through to Wellington to seek advice and information.
Police also looked at footwear impression databases from Australia, the United States and Canada which contained hundreds of thousands of shoes, but no matches were found.
The breakthrough came when Proline brand dive boots were identified as a match by Detective James Bugg almost a year after Mr Guy was murdered.
The Crown alleges Macdonald bought a pair of size nine Proline dive boots at cost price from his father's Palmerston North store, Hunting and Fishing, and disposed of them after the murder.
The boots have never been found.
Mr Howell said the Proline boots had several identifying characteristics but the wavy pattern was "one of the stand-out features''.
He looked at about 30,000 shoes online to rule out any other contenders.
"There were no other footwear of any description that matched those impressions.''
More than 5500 pairs of Proline dive boot were made in Taiwan for a United States-based company from 2000 to 2006.
Mr Howell found more than 20 websites advertising the Proline dive boots, but none were in New Zealand and most linked back to one in the United States.
The court earlier heard from hunting equipment importer Richard Stephens, whose company supplied Hunting and Fishing with Proline dive boots in 2003.
He imported 305 pairs of the boots, 281 of which were sold at Hunting and Fishing stores throughout New Zealand.
Fifty-four of those pairs were in size nine, of which five were sold at the Manawatu store.
Under cross-examination by defence lawyer Greg King, Mr Stephens agreed 29 pairs of boots he imported were unaccounted for.
He said his company was the only one to import that particular model of Proline dive boots, but he agreed he could not stop someone buying a pair over the internet.
The court was shown a photo of Stewart Island hunting trip that Ewen and Kerry Macdonald went on in March 2004.
Foxton farmer Graeme Hunt, who took the photo, said a diving boot shown near Macdonald in the photo was not his own.
Another photo from a March 2005 trip to Stewart Island showed Macdonald wearing a pair of dive boots at a camping site.
Hunting and Fishing sales and marketing manager Andrew Tannock read from an autumn 2004 catalogue that said the Proline dive boots were quiet, which made it easier to "sneak in on'' animals while hunting.
He said a lot of good hunters liked to walk as softly as they could because deer had "a very acute sense of hearing''.
Under cross-examination, Mr Tannock agreed the boots would pretty good footwear for a burglar.
The trial before Justice Simon France and a jury of 11 continues tomorrow with more evidence expected from Mr Neale.
